A team from the Institute of Oceanology, Chinese Academy of Sciences, has made a new breakthrough in silver pomfret genomics. They released the first high-quality chromosome-level reference genome for this important and economically valuable fish species in China, their findings were published online in Nature's Scientific Data.
Chinese silver pomfret (Pampus argenteus) belongs to the order Carangiformes, family Carangidae, genus Pampus. It is widely distributed in coastal waters of the Northwest Pacific, found from the northern part of the South China Sea to the coasts of Japan, Korea and Russia. With its delicate flesh and high fat content, silver pomfret is an important economic fish species in China, having extremely high economic value.
Courtesy of Institute of Oceanology, Chinese Academy of Sciences
The supply of silver pomfret is highly dependent on fishery catches. Since the 1980s, the fishing intensity in the Chinese seas has been continuously increasing. In recent years, the annual catch of Scatophagus species, mainly silver pomfret, has exceeded 300,000 tons, posing a great risk of depletion of silver pomfret wild resources.
At present, China has made groundbreaking progress in the artificial breeding and farming techniques of silver pomfret, which is of great significance for the protection and restoration of silver pomfret wild resources. However, silver pomfret is extremely sensitive to environmental changes and is prone to stress death during transportation and farming, which hinders the development of the silver pomfret farming industry. In addition, silver pomfret has specialized morphology, its body is extremely laterally flattened, and it has no pelvic fins. The foregut has a special esophageal lateral sac structure, which is a key evolutionary characteristic of the suborder Scatophagoidei. It is an important trait for silver pomfret to adapt to feeding on small crustaceans and jellyfish.
Previously, a research team led by Researcher Liu Jing from the Institute of Oceanology, based on the global mitochondrial genome data of Scatophagus and their morphological and distribution characteristics, clarified for the first time the formation and evolutionary history of the diversity and geographic distribution of Scatophagus species in the world. The results showed that currently, there are seven valid species of Scatophagus in the world: namely, silver pomfret, Chinese pomfret, grey pomfret, Liu's pomfret, rare pomfret, feather pomfret, and plain pomfret. The sickle pomfret reported in the past literature is a synonym of silver pomfret.
Based on previous studies, the research team used relevant sequencing technologies for comprehensive deep sequencing and assembly of the Asian sea bass genome. They obtained the first high-quality chromosome-level reference genome of Asian sea bass in the world, resulting in 24 chromosome monomer sequences of Asian sea bass. The study precisely revealed that the genome size of Asian sea bass is 518.06 Mbp, with the assembled genome Contig N50 length reaching 20.47 Mbp and the Scaffold N50 length reaching 22.86 Mbp. The genome completeness is extremely high, reaching the chromosome level. Repetitive sequences account for 13.45% of the genome, and 24,696 protein-coding genes were obtained. The completeness assessment indicator BUSCO value of the genome is as high as 98.90%. These research results provide a high-quality reference genome foundation for in-depth analysis of the evolution of esophageal lateral sac and pelvic fin deficiency traits in Asian sea bass, germplasm genetic resource assessment, breeding of resistant varieties, and sustainable utilization of Asian sea bass fishery resources.
This study was supported by the National Natural Science Foundation of China and the Strategic Priority Research Program of the Chinese Academy of Sciences (B).
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